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softenv.txt
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softenv.txt
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#!/usr/bin/env -S bash -l
set -e
# Conda versions as of 2021-10-19
# conda list:
# python 3.9.7 hb7a2778_1_cpython conda-forge
# star 2.7.9a h9ee0642_0 bioconda
# samtools 1.13 h8c37831_0 bioconda
# openjdk 8.0.302 h7f98852_0 conda-forge
# gatk4 4.2.2.0 hdfd78af_1 bioconda
# bedtools 2.30.0 h7d7f7ad_2 bioconda
# igvtools 2.5.3 hdfd78af_1 bioconda
#
#
# command line query:
# python -V Python 3.9.7
# sra-toolkit 2.11.0
#
# STAR --version 2.7.9a
#
# samtools --version samtools 1.13
# Using htslib 1.13
#
# java -version openjdk version "1.8.0_302"
#
# gatk -version The Genome Analysis Toolkit (GATK) v4.2.2.0
# HTSJDK Version: 2.24.1
# Picard Version: 2.25.4
#
# bedtools --version bedtools v2.30.0
#
# igvtools version IGV Version 2.5.3 05/29/2019 10:59 AM
# Using bundled JDK
#
# $CONDA_PREFIX/share/igvtools-2.5.3-1/jdk-11/bin/java -version
# openjdk version "11.0.2" 2019-01-15
#
# Install miniconda
# wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
# install conda
if ! command -v conda&> /dev/null; then
echo "installing miniconda..."
wget https://repo.anaconda.com/miniconda/Miniconda3-py39_4.9.2-Linux-x86_64.sh
bash Miniconda3-py39_4.9.2-Linux-x86_64.sh -b
rm -f Miniconda3-py39_4.9.2-Linux-x86_64.sh
~/miniconda3/bin/conda init
echo "miniconda installed. restart terminal."
exit 0
else
echo "miniconda installed already."
fi
# be sure to restart terminal to allow conda to start
conda create -y -n xskew
sleep 2
conda activate xskew
conda install -y -c conda-forge -c bioconda biopython python=3.9.7 snakemake=6.8.0 star gatk4 samtools bamtools bedtools igvtools openjdk
# Move jdk-11 to igvtoolsdir so launch script notices it as local JDK
# vs. JDK8 which is used for gatk4
cd ~/src
wget https://data.broadinstitute.org/igv/projects/downloads/2.5/IGV_Linux_2.5.3.zip
unzip IGV_Linux_2.5.3.zip
mv IGV_Linux_2.5.3/jdk-11 $CONDA_PREFIX/share/igvtools-2.5.3-1/
# #download sratoolkit, link binaries within conda environment
# linux/centos
cd $CONDA_PREFIX
wget https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.11.0/sratoolkit.2.11.0-centos_linux64.tar.gz
tar -xvzf sratoolkit.2.11.0-centos_linux64.tar.gz
cd bin
ln -s ../sratoolkit.2.11.0-centos_linux64/bin/* ./
echo "done. xskew env installed. 'conda activate xskew' to enable..."